.TH g_x2top 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
.SH NAME
g_x2top - generates a primitive topology from coordinates 

.B VERSION 4.5
.SH SYNOPSIS
\f3g_x2top\fP
.BI "\-f" " conf.gro "
.BI "\-o" " out.top "
.BI "\-r" " out.rtp "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-ff" " string "
.BI "\-[no]v" ""
.BI "\-nexcl" " int "
.BI "\-[no]H14" ""
.BI "\-[no]alldih" ""
.BI "\-[no]remdih" ""
.BI "\-[no]pairs" ""
.BI "\-name" " string "
.BI "\-[no]pbc" ""
.BI "\-[no]pdbq" ""
.BI "\-[no]param" ""
.BI "\-[no]round" ""
.BI "\-kb" " real "
.BI "\-kt" " real "
.BI "\-kp" " real "
.SH DESCRIPTION
\&x2top generates a primitive topology from a coordinate file.
\&The program assumes all hydrogens are present when defining
\&the hybridization from the atom name and the number of bonds.
\&The program can also make an rtp entry, which you can then add
\&to the rtp database.


\&When \fB \-param\fR is set, equilibrium distances and angles
\&and force constants will be printed in the topology for all
\&interactions. The equilibrium distances and angles are taken
\&from the input coordinates, the force constant are set with
\&command line options.
\&The force fields somewhat supported currently are:


\&G53a5  GROMOS96 53a5 Forcefield (official distribution)


\&oplsaa OPLS\-AA/L all\-atom force field (2001 aminoacid dihedrals)


\&The corresponding data files can be found in the library directory
\&with name atomname2type.n2t. Check chapter 5 of the manual for more
\&information about file formats. By default the forcefield selection
\&is interactive, but you can use the \fB \-ff\fR option to specify
\&one of the short names above on the command line instead. In that
\&case pdb2gmx just looks for the corresponding file.


.SH FILES
.BI "\-f" " conf.gro" 
.B Input
 Structure file: gro g96 pdb tpr etc. 

.BI "\-o" " out.top" 
.B Output, Opt.
 Topology file 

.BI "\-r" " out.rtp" 
.B Output, Opt.
 Residue Type file used by pdb2gmx 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 0" 
 Set the nicelevel

.BI "\-ff"  " string" " oplsaa" 
 Force field for your simulation. Type "select" for interactive selection.

.BI "\-[no]v"  "no    "
 Generate verbose output in the top file.

.BI "\-nexcl"  " int" " 3" 
 Number of exclusions

.BI "\-[no]H14"  "yes   "
 Use 3rd neighbour interactions for hydrogen atoms

.BI "\-[no]alldih"  "no    "
 Generate all proper dihedrals

.BI "\-[no]remdih"  "no    "
 Remove dihedrals on the same bond as an improper

.BI "\-[no]pairs"  "yes   "
 Output 1\-4 interactions (pairs) in topology file

.BI "\-name"  " string" " ICE" 
 Name of your molecule

.BI "\-[no]pbc"  "yes   "
 Use periodic boundary conditions.

.BI "\-[no]pdbq"  "no    "
 Use the B\-factor supplied in a pdb file for the atomic charges

.BI "\-[no]param"  "yes   "
 Print parameters in the output

.BI "\-[no]round"  "yes   "
 Round off measured values

.BI "\-kb"  " real" " 400000" 
 Bonded force constant (kJ/mol/nm2)

.BI "\-kt"  " real" " 400   " 
 Angle force constant (kJ/mol/rad2)

.BI "\-kp"  " real" " 5     " 
 Dihedral angle force constant (kJ/mol/rad2)

.SH KNOWN PROBLEMS
\- The atom type selection is primitive. Virtually no chemical knowledge is used

\- Periodic boundary conditions screw up the bonding

\- No improper dihedrals are generated

\- The atoms to atomtype translation table is incomplete (atomname2type.n2t files in the data directory). Please extend it and send the results back to the GROMACS crew.

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
